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https://www.readbyqxmd.com/read/28538156/a-simple-marker-assisted-3d-nanometer-drift-correction-method-for-superresolution-microscopy
#1
Hongqiang Ma, Jianquan Xu, Jingyi Jin, Yi Huang, Yang Liu
High-precision fluorescence microscopy such as superresolution imaging or single-particle tracking often requires an online drift correction method to maintain the stability of the three-dimensional (3D) position of the sample at a nanometer precision throughout the entire data acquisition process. Current online drift correction methods require modification of the existing two-dimensional (2D) fluorescence microscope with additional optics and detectors, which can be cumbersome and limit its use in many biological laboratories...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28535583/molecular-testing-of-brain-tumor
#2
REVIEW
Sung-Hye Park, Jaekyung Won, Seong-Ik Kim, Yujin Lee, Chul-Kee Park, Seung-Ki Kim, Seung-Hong Choi
The World Health Organization (WHO) classification of central nervous system (CNS) tumors was revised in 2016 with a basis on the integrated diagnosis of molecular genetics. We herein provide the guidelines for using molecular genetic tests in routine pathological practice for an accurate diagnosis and appropriate management. While astrocytomas and IDH-mutant (secondary) glioblastomas are characterized by the mutational status of IDH, TP53 , and ATRX , oligodendrogliomas have a 1p/19q codeletion and mutations in IDH, CIC , FUBP1 , and the promoter region of telomerase reverse transcriptase ( TERTp )...
May 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/28535443/independent-validation-of-body-fluid-specific-cpg-markers-and-construction-of-a-robust-multiplex-assay
#3
Hannah Holtkötter, Vanessa Beyer, Kristina Schwender, Alina Glaub, Kristina Schulze Johann, Marianne Schürenkamp, Ursula Sibbing, Sabrina Banken, Peter Wiegand, Heidi Pfeiffer, Lynn Dennany, Marielle Vennemann, Marielle Vennemann
Potential forensic use of tissue-specific DNA methylation markers has recently been discussed for the identification of the biological source of a stain. In this study 13 promising markers were evaluated to identify suitable candidate markers for the development of a robust and reliable multiplex assay. The results of this study suggest that a combination of only four highly informative markers will be enough for clear body fluid identification. A multiplex assay was developed for the identification of menstrual blood, saliva, semen, and venous blood...
May 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28535204/colocalization-of-receptors-for-shiga-toxins-with-lipid-rafts-in-primary-human-renal-glomerular-endothelial-cells-and-influence-of-d-pdmp-on-synthesis-and-distribution-of-glycosphingolipid-receptors
#4
Nadine Legros, Gottfried Pohlentz, Jana Runde, Stefanie Dusny, Hans-Ulrich Humpf, Helge Karch, Johannes Müthing
Damage of human renal glomerular endothelial cells (HRGECs) of the kidney represents the linchpin in the pathogenesis of the hemolytic uremic syndrome (HUS) caused by Shiga toxins (Stxs) of enterohemorrhagic Escherichia coli (EHEC). We performed a comprehensive structural analysis of the Stx receptor glycosphingolipids (GSLs) globotriaosylceramide (Gb3Cer, Galα4alβ4Glcβ1Cer) and globotetraosylceramide (Gb4Cer, GalNAcβ3Galα4Galβ4Glcβ1Cer) and their distribution in lipid raft analogue detergent-resistant membranes (DRMs) and nonDRMs prepared from primary HRGECs...
May 23, 2017: Glycobiology
https://www.readbyqxmd.com/read/28533524/enhancing-the-genome-editing-toolbox-genome-wide-crispr-arrayed-libraries
#5
Emmanouil Metzakopian, Alex Strong, Vivek Iyer, Alex Hodgkins, Konstantinos Tzelepis, Liliana Antunes, Mathias J Friedrich, Qiaohua Kang, Teresa Davidson, Jacob Lamberth, Christina Hoffmann, Gregory D Davis, George S Vassiliou, William C Skarnes, Allan Bradley
CRISPR-Cas9 technology has accelerated biological research becoming routine for many laboratories. It is rapidly replacing conventional gene editing techniques and has high utility for both genome-wide and gene-focussed applications. Here we present the first individually cloned CRISPR-Cas9 genome wide arrayed sgRNA libraries covering 17,166 human and 20,430 mouse genes at a complexity of 34,332 sgRNAs for human and 40,860 sgRNAs for the mouse genome. For flexibility in generating stable cell lines the sgRNAs have been cloned in a lentivirus backbone containing PiggyBac transposase recognition elements together with fluorescent and drug selection markers...
May 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28531339/limtox-a-web-tool-for-applied-text-mining-of-adverse-event-and-toxicity-associations-of-compounds-drugs-and-genes
#6
Andres Cañada, Salvador Capella-Gutierrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger
A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531169/expression-of-liver-receptor-homolog-1-lrh-1-in-villi-and-decidua-of-patients-with-unexplained-recurrent-spontaneous-abortion
#7
Zhiyan Xu, Xiangqing Hou, Hongtao Lv, Binghui Sun, Yingying Cui, Ling Liu, Fengnian Rong
BACKGROUND In view of the important function of nuclear receptor liver receptor homolog 1 (LRH 1) in various biological processes and the physiological changes accompanying unexplained recurrent spontaneous abortion (USRA), our study was carried out to investigate the potential roles of LRH-1 in USRA. MATERIAL AND METHODS Thirty patients with URSA at early the early state of pregnancy were selected, and 30 patients with normal early pregnancy were also selected from Aug 2015 to Sep 2016 as a control group. The expression of LRH-1 protein in decidua and villi were detected by immunohistochemistry and Western blot analysis, and the expression of LRH-1 mRNA was detected by RT-PCR...
May 22, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28531107/analysis-of-gene-expression-signatures-in-cancer-associated-stroma-from-canine-mammary-tumours-reveals-molecular-homology-to-human-breast-carcinomas
#8
Julia Ettlin, Elena Clementi, Parisa Amini, Alexandra Malbon, Enni Markkanen
Cancer-associated stroma (CAS) plays a key role in cancer initiation and progression. Spontaneously occurring canine mammary carcinomas are viewed as excellent models of human breast carcinomas. Considering the importance of CAS for human cancer, it likely plays a central role in canine tumours as well. So far, however, canine CAS lacks characterisation, and it remains unclear whether the biology between CAS from canine and human tumours is comparable. In this proof-of-principle study, using laser-capture microdissection, we isolated CAS and normal stroma from 13 formalin-fixed paraffin embedded canine simple mammary carcinomas and analysed the expression of seven known human CAS markers by RT-qPCR (Reverse Transcription quantitative PCR) and validated some targets by immunohistochemistry...
May 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28530531/the-complexity-of-dek-signaling-in-cancer-progression
#9
Yong Teng, Liwei Lang, Catherine E Jauregui
The DNA binding protein and chromatin structural regulator DEK regulates many cellular processes. These include proliferation, differentiation, apoptosis, senescence, DNA repairing and the maintenance of stem cell phenotype. DEK is increasingly recognized as a crucial player in many steps of cancer initiation and progression, and is precisely regulated by abundant promoting and inhibiting factors directly or indirectly. DEK may serve as an architectural modulating protein to regulate the expression and function of multiple human genes in cancer cells...
May 21, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28530125/pro-inflammatory-activation-of-primary-microglia-and-macrophages-increases-18%C3%A2-kda-translocator-protein-expression-in-rodents-but-not-humans
#10
David R Owen, Nehal Narayan, Lisa Wells, Luke Healy, Erica Smyth, Eugenii A Rabiner, Dylan Galloway, John B Williams, Joshua Lehr, Harpreet Mandhair, Laura An Peferoen, Peter C Taylor, Sandra Amor, Jack P Antel, Paul M Matthews, Craig S Moore
The 18kDa Translocator Protein (TSPO) is the most commonly used tissue-specific marker of inflammation in positron emission tomography (PET) studies. It is expressed in myeloid cells such as microglia and macrophages, and in rodent myeloid cells expression increases with cellular activation. We assessed the effect of myeloid cell activation on TSPO gene expression in both primary human and rodent microglia and macrophages in vitro, and also measured TSPO radioligand binding with (3)H-PBR28 in primary human macrophages...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28529924/regulation-of-cancer-cell-responsiveness-to-ionizing-radiation-treatment-by-cyclic-amp-response-element-binding-nuclear-transcription-factor
#11
REVIEW
Francesca D'Auria, Lucia Centurione, Maria Antonietta Centurione, Antonio Angelini, Roberta Di Pietro
Cyclic AMP response element binding (CREB) protein is a member of the CREB/activating transcription factor (ATF) family of transcription factors that play an important role in the cell response to different environmental stimuli leading to proliferation, differentiation, apoptosis, and survival. A number of studies highlight the involvement of CREB in the resistance to ionizing radiation (IR) therapy, demonstrating a relationship between IR-induced CREB family members' activation and cell survival. Consistent with these observations, we have recently demonstrated that CREB and ATF-1 are expressed in leukemia cell lines and that low-dose radiation treatment can trigger CREB activation, leading to survival of erythro-leukemia cells (K562)...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/28528700/directed-differentiation-of-human-pluripotent-stem-cells-to-microglia
#12
Panagiotis Douvaras, Bruce Sun, Minghui Wang, Ilya Kruglikov, Gregory Lallos, Matthew Zimmer, Cecile Terrenoire, Bin Zhang, Sam Gandy, Eric Schadt, Donald O Freytes, Scott Noggle, Valentina Fossati
Microglia, the immune cells of the brain, are crucial to proper development and maintenance of the CNS, and their involvement in numerous neurological disorders is increasingly being recognized. To improve our understanding of human microglial biology, we devised a chemically defined protocol to generate human microglia from pluripotent stem cells. Myeloid progenitors expressing CD14/CX3CR1 were generated within 30 days of differentiation from both embryonic and induced pluripotent stem cells (iPSCs). Further differentiation of the progenitors resulted in ramified microglia with highly motile processes, expressing typical microglial markers...
May 18, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28528141/portland-cement-induces-human-periodontal-ligament-cells-to-differentiate-by-upregulating-mir-146a
#13
Min-Ching Wang, Li-Yin Yeh, Wen-Yu Shih, Wan-Chun Li, Kuo-Wei Chang, Shu-Chun Lin
BACKGROUND/PURPOSE: Bioaggregates such as Portland cement (PC) can be an economical alternative for mineral trioxide aggregate (MTA) with additional benefit of less discoloration. MTA has been known to induce differentiations of several dental cells. MicroRNAs are important regulators of biological processes, including differentiation, physiologic homeostasis, and disease progression. This study is to explore how PC enhances the differentiation of periodontal ligament (PDL) cells in microRNAs level...
May 18, 2017: Journal of the Formosan Medical Association, Taiwan Yi Zhi
https://www.readbyqxmd.com/read/28527094/circulating-tumor-dna-measurement-by-picoliter-droplet-based-digital-pcr-and-vemurafenib-plasma-concentrations-in-patients-with-advanced-braf-mutated-melanoma
#14
Fanny Garlan, Benoit Blanchet, Nora Kramkimel, Alicja Puszkiel, Jean-Louis Golmard, Gaelle Noe, Nicolas Dupin, Pierre Laurent-Puig, Michel Vidal, Valerie Taly, Audrey Thomas-Schoemann
BACKGROUND: Circulating tumor DNA (ctDNA) has been reported as a prognostic marker in melanoma. In BRAF V600-mutant melanoma, a plasma under-exposure to vemurafenib could favor emerging resistance but no biological data are available to support this hypothesis. OBJECTIVE: We aimed to investigate the relationship between vemurafenib plasma concentrations and the ctDNA plasma concentration during follow-up of BRAF-mutated melanoma patients. PATIENTS AND METHODS: Eleven patients treated with single-agent vemurafenib for advanced BRAF V600-mutant melanoma were analyzed in an exploratory monocentric study...
May 19, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/28527052/action-mechanisms-of-onabotulinum-toxin-a-hints-for-selection-of-eligible-patients
#15
Carlo Lovati, Luca Giani
In the past few decades, the so-feared botulinum toxin has conversely acquired the role of a ever more versatile therapeutic substance, used in an increasing number of pathological situations, including chronic headache and more precisely in the prophylaxis of chronic migraine. The medical use of botulinum toxin allowed to better understand its multiple mechanisms of action. Investigations about the pathophysiology of primary and secondary headaches has shown a series of common biological elements that frequently are also targets of the action of botulinum toxin...
May 2017: Neurological Sciences
https://www.readbyqxmd.com/read/28526992/epithelial-mesenchymal-transition-emt-in-metastatic-breast-cancer-in-omani-women
#16
Ritu Lakhtakia, Adil Aljarrah, Muhammad Furrukh, Shyam S Ganguly
Breast cancer (BC) in Oman affects younger women and has a more aggressive course. Clinical and biological variables like age, pregnancy, tumor size, type, grade, receptor expression and proliferation predict disease aggression but there is no direct predictor of metastasis except lymphovascular invasion. Epithelial-mesenchymal transition (EMT) is characterized by epithelial cells losing epithelial and acquiring mesenchymal morpho-immunophenotypic characteristics. In tumors, EMT-like transitions may signify a metastatic phenotype and have features in common with cancer stem cells (CSC) which show resistance to chemotherapy...
May 19, 2017: Cancer Microenvironment: Official Journal of the International Cancer Microenvironment Society
https://www.readbyqxmd.com/read/28526892/stereotactic-core-needle-breast-biopsy-marker-migration-an-analysis-of-factors-contributing-to-immediate-marker-migration
#17
Ashali Jain, Maria Khalid, Muhammad M Qureshi, Dianne Georgian-Smith, Jonah A Kaplan, Karen Buch, Mark W Grinstaff, Ariel E Hirsch, Neely L Hines, Stephan W Anderson, Katherine M Gallagher, David D B Bates, B Nicolas Bloch
OBJECTIVES: To evaluate breast biopsy marker migration in stereotactic core needle biopsy procedures and identify contributing factors. METHODS: This retrospective study analyzed 268 stereotactic biopsy markers placed in 263 consecutive patients undergoing stereotactic biopsies using 9G vacuum-assisted devices from August 2010-July 2013. Mammograms were reviewed and factors contributing to marker migration were evaluated. Basic descriptive statistics were calculated and comparisons were performed based on radiographically-confirmed marker migration...
May 19, 2017: European Radiology
https://www.readbyqxmd.com/read/28526870/time-course-responses-of-circulating-micrornas-to-three-resistance-training-protocols-in-healthy-young-men
#18
Shufang Cui, Biao Sun, Xin Yin, Xia Guo, Dingming Chao, Chunni Zhang, Chen-Yu Zhang, Xi Chen, Jizheng Ma
Circulating microRNAs (c-miRNAs) in human plasma have been described as a potential marker of exercise. The present study investigated the effects of three acute resistance training (RT) protocols on the time-course changes of the c-miRNAs profiles in young males. The subjects (n = 45) were randomly divided into three groups: muscular strength endurance (SE), muscular hypertrophy (MH) and maximum strength (MS). Venous blood samples were obtained before exercise and immediately, 1 h and 24 h after each RT protocol to assess the following biological parameters: c-miRNAs, anabolic and catabolic hormones, inflammatory cytokines and muscle damage markers...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526063/targeting-the-cxcr4-pathway-using-a-novel-anti-cxcr4-igg1-antibody-pf-06747143-in-chronic-lymphocytic-leukemia
#19
Manoj K Kashyap, Carlos I Amaya-Chanaga, Deepak Kumar, Brett Simmons, Nanni Huser, Yin Gu, Max Hallin, Kevin Lindquist, Rolla Yafawi, Michael Y Choi, Ale-Ali Amine, Laura Z Rassenti, Cathy Zhang, Shu-Hui Liu, Tod Smeal, Valeria R Fantin, Thomas J Kipps, Flavia Pernasetti, Januario E Castro
BACKGROUND: The CXCR4-CXCL12 axis plays an important role in the chronic lymphocytic leukemia (CLL)-microenvironment interaction. Overexpression of CXCR4 has been reported in different hematological malignancies including CLL. Binding of the pro-survival chemokine CXCL12 with its cognate receptor CXCR4 induces cell migration. CXCL12/CXCR4 signaling axis promotes cell survival and proliferation and may contribute to the tropism of leukemia cells towards lymphoid tissues and bone marrow...
May 19, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28525568/scenery-a-web-application-for-causal-network-reconstruction-from-cytometry-data
#20
Georgios Papoutsoglou, Giorgos Athineou, Vincenzo Lagani, Iordanis Xanthopoulos, Angelika Schmidt, Szabolcs Éliás, Jesper Tegnér, Ioannis Tsamardinos
Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data...
May 19, 2017: Nucleic Acids Research
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